Figure 1: Deep sequencing reveals low sequence variation in haemagglutinin of influenza virus stocks. | Nature Communications

Figure 1: Deep sequencing reveals low sequence variation in haemagglutinin of influenza virus stocks.

From: Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses

Figure 1

We used deep sequencing to probe the nucleotide diversity of the (a) VN1203-HA(3)-CA04 and (b) VN1203-HA(4)-CA04 virus stocks used in mammalian transmission experiments. Individual HA sequence reads were mapped to a consensus HA sequence derived from the isolate A/Vietnam/1203/2004 (H5N1). SNPs were enumerated as described in Methods. No variants were detected below 0.01%. The frequency of variants at each site is presented as either closed circles (nonsynonymous substitutions) or open squares (synonymous substitutions). Mutations previously reported in association with mammalian transmission are highlighted in red: VN1203-HA(3)-CA04: N158D (nt 536), N224K (nt 736) and Q226L (nt 741) and VN1203-HA(4)-CA04: N158D (nt 536), N224K (nt 736), Q226L (nt 741) and T318I (nt 1,020). A synonymous mutation at nucleotide position 1555 that was not present in the plasmid used to generate viruses by reverse genetics was detected in each virus stock after harvest and before infection of ferrets.

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